Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	E	T	E	T	G	R	Y	S	D	T	L	R	S	A	L	V	S	L	D	G	D	N	A	W	A	L	S	E	S	W	C	G	T	I	Q	W	I	C	P	S	P	Y	R	P	H	H	G	R	K	N	W	F	L	G	I	G	R	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																																?	?	?	?	?	?	?	?	?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	A	D	E	Q	E	Q	S	D	A	I	R	Y	E	T	L	R	S	S	G	P	G	G	Q	H	V	N	K	T	D	S	A	V	R	A	T	H	L	A	S	G	I	S	V	K	V	Q	S	E	R	S	Q	H	A	N	K	R	L	A	R
Secondary structure
SS confidence
Disorder		?	?															?	?		?	?			?																										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.
Sequence		L	L	I	A	W	K	L	E	Q	Q	Q	Q	E	N	S	A	A	L	K	S	Q	R	R	M	F	H	H	Q	I	E	R	G	N	P	R	R	T	F	T	G	M	A	F	I	E	G
Secondary structure
SS confidence
Disorder													?	?	?	?												?	?	?	?	?	?	?	?	?		?			?	?	?	?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 3d5c chain X Region: 1 - 164 Aligned: 162 Modelled: 164 Confidence: 100.0% Identity: 25% PDB header:ribosome Chain: X: PDB Molecule:peptide chain release factor 1; PDBTitle: structural basis for translation termination on the 70s ribosome. this2 file contains the 30s subunit, release factor 1 (rf1), two trna, and3 mrna molecules of the second 70s ribosome. the entire crystal4 structure contains two 70s ribosomes as described in remark 400. Phyre2 PDB 2ihr chain 1 Region: 1 - 164 Aligned: 162 Modelled: 164 Confidence: 100.0% Identity: 30% PDB header:translation Chain: 1: PDB Molecule:peptide chain release factor 2; PDBTitle: rf2 of thermus thermophilus Phyre2 PDB 1gqe chain A Region: 1 - 164 Aligned: 163 Modelled: 159 Confidence: 100.0% Identity: 28% Fold: Release factor Superfamily: Release factor Family: Release factor Phyre2 PDB 2b3t chain B domain 1 Region: 1 - 161 Aligned: 148 Modelled: 161 Confidence: 100.0% Identity: 28% Fold: Release factor Superfamily: Release factor Family: Release factor Phyre2 PDB 1rq0 chain A Region: 1 - 164 Aligned: 149 Modelled: 164 Confidence: 100.0% Identity: 30% Fold: Release factor Superfamily: Release factor Family: Release factor Phyre2 PDB 1zbt chain A Region: 1 - 164 Aligned: 150 Modelled: 162 Confidence: 100.0% Identity: 16% PDB header:translation Chain: A: PDB Molecule:peptide chain release factor 1; PDBTitle: crystal structure of peptide chain release factor 1 (rf-1) (smu.1085)2 from streptococcus mutans at 2.34 a resolution Phyre2 PDB 2jy9 chain A Region: 59 - 131 Aligned: 73 Modelled: 73 Confidence: 99.9% Identity: 32% PDB header:hydrolase Chain: A: PDB Molecule:putative trna hydrolase domain; PDBTitle: nmr structure of putative trna hydrolase domain from2 salmonella typhimurium. northeast structural genomics3 consortium target str220 Phyre2 PDB 2jva chain A Region: 57 - 132 Aligned: 76 Modelled: 76 Confidence: 99.9% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:peptidyl-trna hydrolase domain protein; PDBTitle: nmr solution structure of peptidyl-trna hydrolase domain protein from2 pseudomonas syringae pv. tomato. northeast structural genomics3 consortium target psr211 Phyre2 PDB 1j26 chain A Region: 61 - 131 Aligned: 71 Modelled: 71 Confidence: 99.9% Identity: 32% Fold: dsRBD-like Superfamily: Peptidyl-tRNA hydrolase domain-like Family: Peptidyl-tRNA hydrolase domain Phyre2 PDB 2ctk chain A domain 1 Region: 80 - 139 Aligned: 60 Modelled: 60 Confidence: 42.8% Identity: 17% Fold: Eukaryotic type KH-domain (KH-domain type I) Superfamily: Eukaryotic type KH-domain (KH-domain type I) Family: Eukaryotic type KH-domain (KH-domain type I) Phyre2 PDB 1s1h chain I Region: 42 - 61 Aligned: 20 Modelled: 20 Confidence: 16.4% Identity: 5% PDB header:ribosome Chain: I: PDB Molecule:40s ribosomal protein s16; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. Phyre2 PDB 2ctj chain A domain 1 Region: 80 - 131 Aligned: 52 Modelled: 52 Confidence: 15.9% Identity: 15% Fold: Eukaryotic type KH-domain (KH-domain type I) Superfamily: Eukaryotic type KH-domain (KH-domain type I) Family: Eukaryotic type KH-domain (KH-domain type I) Phyre2 PDB 2yrv chain A Region: 37 - 79 Aligned: 40 Modelled: 43 Confidence: 13.4% Identity: 10% PDB header:transcription Chain: A: PDB Molecule:at-rich interactive domain-containing protein 4a; PDBTitle: solution structure of the rbb1nt domain of human2 rb(retinoblastoma)-binding protein 1 Phyre2 PDB 2axy chain A domain 1 Region: 80 - 129 Aligned: 50 Modelled: 50 Confidence: 12.4% Identity: 22% Fold: Eukaryotic type KH-domain (KH-domain type I) Superfamily: Eukaryotic type KH-domain (KH-domain type I) Family: Eukaryotic type KH-domain (KH-domain type I) Phyre2 PDB 1ztg chain D Region: 80 - 129 Aligned: 50 Modelled: 50 Confidence: 11.9% Identity: 18% PDB header:dna, rna binding protein/dna Chain: D: PDB Molecule:poly(rc)-binding protein 1; PDBTitle: human alpha polyc binding protein kh1 Phyre2 PDB 2vqe chain I domain 1 Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 11.0% Identity: 14% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Translational machinery components Phyre2 PDB 1kgi chain A Region: 1 - 53 Aligned: 43 Modelled: 53 Confidence: 10.2% Identity: 12% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 2gy9 chain I domain 1 Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 10.2% Identity: 14% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Translational machinery components Phyre2 PDB 2jzx chain A Region: 80 - 131 Aligned: 52 Modelled: 52 Confidence: 9.8% Identity: 21% PDB header:rna binding protein Chain: A: PDB Molecule:poly(rc)-binding protein 2; PDBTitle: pcbp2 kh1-kh2 domains Phyre2 PDB 2x9q chain A Region: 18 - 46 Aligned: 29 Modelled: 29 Confidence: 9.7% Identity: 14% PDB header:ligase Chain: A: PDB Molecule:cyclodipeptide synthetase; PDBTitle: structure of the mycobacterium tuberculosis protein, rv2275,2 demonstrates that cyclodipeptide synthetases are related3 to type i trna-synthetases. Phyre2 1 c3d5cX_ 2 c2ihr1_ 3 d1gqea_ 4 d2b3tb1 5 d1rq0a_ 6 c1zbtA_ 7 c2jy9A_ 8 c2jvaA_ 9 d1j26a_ 10 d2ctka1 11 c1s1hI_ 12 d2ctja1 13 c2yrvA_ 14 d2axya1 15 c1ztgD_ 16 d2vqei1 17 d1kgia_ 18 d2gy9i1 19 c2jzxA_ 20 c2x9qA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c3d5cX_ 100.0 25 PDB header:ribosome Chain: X: PDB Molecule:peptide chain release factor 1; PDBTitle: structural basis for translation termination on the 70s ribosome. this2 file contains the 30s subunit, release factor 1 (rf1), two trna, and3 mrna molecules of the second 70s ribosome. the entire crystal4 structure contains two 70s ribosomes as described in remark 400. 2 c2ihr1_ 100.0 30 PDB header:translation Chain: 1: PDB Molecule:peptide chain release factor 2; PDBTitle: rf2 of thermus thermophilus 3 d1gqea_ 100.0 28 Fold:Release factor Superfamily:Release factor Family:Release factor 4 d2b3tb1 100.0 28 Fold:Release factor Superfamily:Release factor Family:Release factor 5 d1rq0a_ 100.0 30 Fold:Release factor Superfamily:Release factor Family:Release factor 6 c1zbtA_ 100.0 16 PDB header:translation Chain: A: PDB Molecule:peptide chain release factor 1; PDBTitle: crystal structure of peptide chain release factor 1 (rf-1) (smu.1085)2 from streptococcus mutans at 2.34 a resolution 7 c2jy9A_ 99.9 32 PDB header:hydrolase Chain: A: PDB Molecule:putative trna hydrolase domain; PDBTitle: nmr structure of putative trna hydrolase domain from2 salmonella typhimurium. northeast structural genomics3 consortium target str220 8 c2jvaA_ 99.9 26 PDB header:hydrolase Chain: A: PDB Molecule:peptidyl-trna hydrolase domain protein; PDBTitle: nmr solution structure of peptidyl-trna hydrolase domain protein from2 pseudomonas syringae pv. tomato. northeast structural genomics3 consortium target psr211 9 d1j26a_ 99.9 32 Fold:dsRBD-like Superfamily:Peptidyl-tRNA hydrolase domain-like Family:Peptidyl-tRNA hydrolase domain 10 d2ctka1 42.8 17 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 11 c1s1hI_ 16.4 5 PDB header:ribosome Chain: I: PDB Molecule:40s ribosomal protein s16; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 12 d2ctja1 15.9 15 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 13 c2yrvA_ 13.4 10 PDB header:transcription Chain: A: PDB Molecule:at-rich interactive domain-containing protein 4a; PDBTitle: solution structure of the rbb1nt domain of human2 rb(retinoblastoma)-binding protein 1 14 d2axya1 12.4 22 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 15 c1ztgD_ 11.9 18 PDB header:dna, rna binding protein/dna Chain: D: PDB Molecule:poly(rc)-binding protein 1; PDBTitle: human alpha polyc binding protein kh1 16 d2vqei1 11.0 14 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 17 d1kgia_ 10.2 12 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 18 d2gy9i1 10.2 14 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 19 c2jzxA_ 9.8 21 PDB header:rna binding protein Chain: A: PDB Molecule:poly(rc)-binding protein 2; PDBTitle: pcbp2 kh1-kh2 domains 20 c2x9qA_ 9.7 14 PDB header:ligase Chain: A: PDB Molecule:cyclodipeptide synthetase; PDBTitle: structure of the mycobacterium tuberculosis protein, rv2275,2 demonstrates that cyclodipeptide synthetases are related3 to type i trna-synthetases. 21 c2zkqi_ not modelled 9.4 7 PDB header:ribosomal protein/rna Chain: I: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 22 c3bbnI_ not modelled 9.0 13 PDB header:ribosome Chain: I: PDB Molecule:ribosomal protein s9; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 23 c1rl2A_ not modelled 8.7 26 PDB header:ribosomal protein Chain: A: PDB Molecule:protein (ribosomal protein l2); PDBTitle: ribosomal protein l2 rna-binding domain from bacillus2 stearothermophilus 24 d1ttaa_ not modelled 8.6 12 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 25 d1viga_ not modelled 8.4 11 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 26 c1tuaA_ not modelled 8.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ape0754; PDBTitle: 1.5 a crystal structure of a protein of unknown function2 ape0754 from aeropyrum pernix 27 c3s2xB_ not modelled 8.2 7 PDB header:transferase Chain: B: PDB Molecule:acetyl-coa synthase subunit alpha; PDBTitle: structure of acetyl-coenzyme a synthase alpha subunit c-terminal2 domain 28 c2eq9C_ not modelled 7.7 35 PDB header:oxidoreductase Chain: C: PDB Molecule:pyruvate dehydrogenase complex, dihydrolipoamide PDBTitle: crystal structure of lipoamide dehydrogenase from thermus thermophilus2 hb8 with psbdb 29 d1wvna1 not modelled 7.4 24 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 30 c2xzmI_ not modelled 7.3 14 PDB header:ribosome Chain: I: PDB Molecule:rps16e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 31 c2eq7C_ not modelled 7.0 18 PDB header:oxidoreductase Chain: C: PDB Molecule:2-oxoglutarate dehydrogenase e2 component; PDBTitle: crystal structure of lipoamide dehydrogenase from thermus thermophilus2 hb8 with psbdo 32 d2ctfa1 not modelled 6.9 12 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 33 c1psbD_ not modelled 6.6 40 PDB header:metal binding protein Chain: D: PDB Molecule:ndr ser/thr kinase-like protein; PDBTitle: solution structure of calcium loaded s100b complexed to a2 peptide from n-terminal regulatory domain of ndr kinase. 34 d2ctea1 not modelled 6.5 11 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 35 c3oqhB_ not modelled 6.5 7 PDB header:ligase Chain: B: PDB Molecule:putative uncharacterized protein yvmc; PDBTitle: crystal structure of b. licheniformis cdps yvmc-blic 36 c2b66D_ not modelled 6.2 33 PDB header:ribosome Chain: D: PDB Molecule:50s ribosomal protein l2; PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf1,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400 37 d1x4na1 not modelled 6.1 17 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 38 d1tfpa_ not modelled 5.5 14 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 39 c3io3A_ not modelled 5.4 33 PDB header:chaperone Chain: A: PDB Molecule:deha2d07832p; PDBTitle: get3 with adp from d. hansenii in closed form 40 d1rl2a1 not modelled 5.4 26 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:C-terminal domain of ribosomal protein L2 41 d1hh2p3 not modelled 5.3 57 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 42 c1psbC_ not modelled 5.2 40 PDB header:metal binding protein Chain: C: PDB Molecule:ndr ser/thr kinase-like protein; PDBTitle: solution structure of calcium loaded s100b complexed to a2 peptide from n-terminal regulatory domain of ndr kinase. 43 c2ftcB_ not modelled 5.1 22 PDB header:ribosome Chain: B: PDB Molecule:mitochondrial ribosomal protein l2; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0